well... the bonded energies are the same, but the 1-4 and nonbonded
interactions are different, especially the coulomb-sr energy. I am
using a direct summation method with no cutoffs to calculate the
electrostatic energy. But the method is consistent between the runs.
So that shouldn't matter should it?
Mark Abraham wrote:
Daniel Cheong wrote:
Thanks for your reply. I thought so too, but i have checked it
several times. The only thing i changed was the "energygrps ="
line in my .mdp file. Then the inclusion and exclusion of energy
monitor groups or just specifying different energy groups will result
in a different total energy. And the larger the energy group, the
greater the difference when compared to the energy calculated with no
energy monitor groups. i use the exact same initial configuration,
topology, index files.
If you use gmxdump to compare your two energy files, what do you get?
Mark
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